SpecProc Activity
SpecProc is a general processing tool for MassLynx data.
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clochardm33
Activity for SpecProc
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SpecProc updated /SpecProc Readme.md
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Henriette K posted a comment on discussion General Discussion
Thanks for all the information. I finally got back to this, sorry for the delay. The layout of the txt file prevented me from using my standard py package for reading csv (or similar) and this was why I was afraid of trying to read it. But after your encouragement I tried again and found a way to ignore the whitespaces and lines starting with ; while still reading the column headers (which are in the ; lines). In case somebody else is in a similar situation, I attached the py file. It's not well...
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clochardM33 posted a comment on discussion General Discussion
Hi, Favourite is that the 3dp numbers end in zero. I don't know what exactly you are doing with the numbers, but 100 samples per batch is very impressive. It's good to see someone using it. The "2 types of output" is in there for exactly what it looks like you are doing, except you have picked the wrong one! If any of this was written down it might have helped, but sadly that never happened. So here is a belated attempt at an explanation. SpecProc was originally written as a mechanism to get peak...
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Hi, This makes sense. I checked the txt files and there number of decimal places are consistent. So, it is really only the xml formatting. Here an extract of my masses from the xml sheet (in the txt file they all have 4 decimal places): <mass>1098.525</mass> <mass>530.788</mass> <mass>539.3013</mass> Per sample batch I have around 100 samples or more. My workflow so far was to open the processing summary (xml) in internet explorer, copy it to excel and save as csv. From there it is straight forward...
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Not sure. By any chance are the one with 4 digits after the decimal place less than mass 1000? Attach an example of what you are looking at pls as it could be any number of things. From memory all numbers are carried through at full precision and there is only ever any rounding in the styling of the xml files. For every xml file there is a corresponding text file which is probably easier to read data from as it drops straight into Excel.
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Hi, what is the format of Peak IDs in the process summary xml? For some ions I have 7 digits for other 8 (can be 3 or 4 digits after the decimal). I checked my ref file with the peak IDs I pass on to specproc and there are far more digits (as I compute them). I just came across this question as I tried to match specproc results with my ion list in a next step (comparing strings). I tried to round or cut my peak list (derived from my ref file), but never get all ions.
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Hi, Thanks for your fast reply! This was it, the extern.inf file was missing. Perfect, thanks a lot!
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Hi, I don't know exactly what is happening, but I think the clue in that they are sliced files. I suspect that there is a missing file or files in the .raw folder. For a reason that I can't explain (as I don't know) this does not stop it opening directly, but does stop it opening with SpecProc (even though behind the scenes SpecProc just pushes the Open button!). If you look in a .raw folder there is a bunch of stuff in there, all prefixed with _ (underscore), such as func001.dat and header.txt If...
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Hi, I've got some problems that certain data files are failing to open in SpecProc. I can open them manually in ML and it's working fine. Failed to open file XXX Attempted 3 retries. At function 1 These specific files are sliced data files from a big original file, which opens fine in both, SpecProc and ML (manual). As I can open them in ML by hand, I don't really know where to look for the culprit. Any help would be great.
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Should have put this out back in April when v1.14 dropped. Anyway, too late to worry about that now. Here's the readme. Version 1.14 This is the release that precisely no one whatsoever asked for! It's packed with new features that are unlikely to make any difference to anyone. Feature changes: 1. Chromatogram Combine Range now supports both "BPI" and "TIC" as a Mass value. In the mass column press b or t to fill with either BPI or TIC. Typing the mass value in still works just as it always did....
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I should have added that the text files look overwhelming in Notepad, but they are set up so they drop straight into Excel. The column layout is predictable so once you know what columns to hide it becomes easily repetitious. The files (both text and xml) contain a lot of information as behind the scenes there is a lot of information (!) and it isn't possible to predict which bits are important to any particular user. So the approach was to stick it all in a file and let you (the user) get what you...
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Hello. Thanks for taking the time to comment. It is really nice to read what you have to say. The results you want are already there, but make sure that in the Options setting of your method (the last tab) you have enabled all the outputs. That is the default setting so they should be on already. Below the SpecProcResults folder there are 2 sets of data (but unless you go looking for it you would only see one of them through the web page view). In addition the most recent processed results are copied...
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The software is working just fine! Thanks for this. I have specified some peak IDs and the summary page looks exactly like I want it to be. Is there a way of easily extracting these information to a txt file or similar? The outputs I found are either in xlm or the single txt files for every sample (in the merged one, there are a lot of other information, so it is possible to read this, but seems unnecessarily cumbersome to extract it from there).
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Update 2018 July 03 Previously you had to select both ResCalc and PeakID if you wanted the Chromatogram masses to be the query. If you didn't then the list stopped after the first entry. That is now fixed. You no longer have to specify ResCalc and PeakID. You only have to specify which one you want.
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Sorry no. It's one range only. This was something I missed a long long time ago, but it is now in the un-fixable catagory.
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Jeremy D posted a comment on discussion General Discussion
I have some flow injection analysis data I would like to process with specproc. As...
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